From a2819cd281bd3ea496ca420d1f75a23bf1741883 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Fri, 19 Jul 2024 07:19:47 -0600
Subject: [PATCH 01/24] (cleanup) Remove swirl_ray.c from restart demo

---
 .../demo/2d/swirl_restart/CMakeLists.txt      |   1 -
 .../demo/2d/swirl_restart/swirl_ray.c         | 372 ------------------
 .../demo/2d/swirl_restart/swirl_user.cpp      |   2 -
 3 files changed, 375 deletions(-)
 delete mode 100644 applications/demo/2d/swirl_restart/swirl_ray.c

diff --git a/applications/demo/2d/swirl_restart/CMakeLists.txt b/applications/demo/2d/swirl_restart/CMakeLists.txt
index 6a146c066..fa17dc10d 100644
--- a/applications/demo/2d/swirl_restart/CMakeLists.txt
+++ b/applications/demo/2d/swirl_restart/CMakeLists.txt
@@ -19,7 +19,6 @@ add_executable(swirl_restart
   swirl_user.cpp 
   swirl.cpp 
   swirl_options.c
-  swirl_ray.c
   $<TARGET_OBJECTS:swirl_f>
 )
 
diff --git a/applications/demo/2d/swirl_restart/swirl_ray.c b/applications/demo/2d/swirl_restart/swirl_ray.c
deleted file mode 100644
index 872b698cf..000000000
--- a/applications/demo/2d/swirl_restart/swirl_ray.c
+++ /dev/null
@@ -1,372 +0,0 @@
-/*
-  Copyright (c) 2012-2022 Carsten Burstedde, Donna Calhoun, Scott Aiton
-  All rights reserved.
-
-  Redistribution and use in source and binary forms, with or without
-  modification, are permitted provided that the following conditions are met:
-
-  * Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-  * Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-  DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#include "swirl_user.h"
-
-#include "../all/advection_user.h"
-
-#include <fclaw_rays.h>
-#include <math.h>
-
-
-typedef struct point
-{
-    double x;
-    double y;
-} point_t;
-
-
-typedef enum 
-{
-    SWIRL_RAY_LINE,
-    SWIRL_RAY_CIRCLE,
-    SWIRL_RAY_TYPE_LAST
-} swirl_ray_type_t;
-
-typedef struct swirl_ray
-{
-    swirl_ray_type_t rtype;
-    double xy[2];
-    union 
-    {
-        struct 
-        {
-            double vec[2];
-        } line;
-        struct 
-        {
-            double radius;
-        } circle;
-    } r;
-} swirl_ray_t;
-
-
-static
-int point_in_quad(point_t p0, point_t pll, point_t pur)
-{
-    int intx = (pll.x <= p0.x) && (p0.x < pur.x);
-    int inty = (pll.y <= p0.y) && (p0.y < pur.y);
-
-    int found = (intx != 0) && (inty != 0);
-    return found;
-}
-
-static
-double distance(point_t p0, point_t p1)
-{
-    double dx = p0.x - p1.x;
-    double dy = p0.y - p1.y;
-    double d = sqrt(dx*dx + dy*dy);
-    return d;
-}
-
-static
-int segment_intersect(point_t p0, point_t p1, 
-                      point_t q0, point_t q1,
-                      point_t *r)
-{
-    /* Find the intersection of two line segments p(s), q(t)
-       with endpoints (p0,p1) and (q0,q1) (in R^2)
-
-       Idea : 
-
-       * Parameterize line segments as
-
-           p(s) = p0 + (p1-p0)*s,  s \in [0,1]
-           q(t) = q0 + (q1-q0)*t,  t \in [0,1]
-
-       * Set p(s)=q(t) to get 2x2 linear system A*x=b in unknowns x=(s,t)
-       * Solve linear system.  Note : Explicit inverse of A is used. 
-       * Check : Segments will intersect if both s,t in [0,1]
-    */
-    /* Coefficients of A */
-    double a11 = p1.x - p0.x;
-    double a21 = p1.y - p0.y;
-    double a12 = -(q1.x - q0.x);
-    double a22 = -(q1.y - q0.y);
-
-    /* Right hand side b */
-    point_t b = {q0.x - p0.x, q0.y - p0.y};
-
-    /* Compute determinant of A */
-    double det = a22*a11 - a12*a21;
-    int found_intersection = 0;
-    if (det == 0)
-    {
-        /* Segments are co-linear or parallel */
-        found_intersection = 0;
-        return 0;
-    }
-
-    /* Solve linear system A*x = b : Use explicit inverse of 
-       2x2 matrix.  */
-    double s = (a22*b.x - a12*b.y)/det;
-    double t = (-a21*b.x + a11*b.y)/det;
-
-    /* Check to see if segments intersect */
-    if ((0 <= s && s < 1) && (0 <= t && t < 1))
-        found_intersection = 1;
-
-    /* Compute intersection of lines (even if segments don't intersect) */
-    r->x = q0.x + (q1.x - q0.x)*t;
-    r->y = q0.y + (q1.y - q0.y)*t;
-
-    return found_intersection;
-}
-
-
-int swirl_intersect_ray (fclaw_domain_t *domain, 
-                         fclaw_patch_t * patch,
-                         int blockno, 
-                         int patchno, 
-                         void *ray, 
-                         double *integral,
-                         void* user)
-{
-
-    fclaw_global_t *glob = (fclaw_global_t*) user;
-
-    /* assert that ray is a valid swirl_ray_t */
-    fclaw_ray_t *fclaw_ray = (fclaw_ray_t *) ray;  
-
-    int id;
-    swirl_ray_t *swirl_ray = (swirl_ray_t*) fclaw_ray_get_ray(fclaw_ray,&id);
-    FCLAW_ASSERT(swirl_ray != NULL);
-    FCLAW_ASSERT(swirl_ray->rtype == SWIRL_RAY_LINE); /* Circles not there yet. */
-
-    if (patchno >= 0) 
-    {
-        /* We are at a leaf and the patch is a valid patch of the domain.
-        * Based on the patch, the domain, the blockno and the information stored
-        * in the swirl_ray_t we defined, we now have to set *integral to be the
-        * contribution of this ray-patch combination to the ray integral.
-        * We should return 1 (even though a leaf return value is ignored). */
-
-        /* This is a dummy example.  We add the ray's x component for each patch.
-        Truly, this example must be updated to compute the exact ray integral. */
-        // *integral = swirl_ray->r.line.vec[0];
-
-        /* DAC : Updated to consider intersection of ray with quadrant.  Contribution to the 
-            integral is the length of the ray segment that in the quad. 
-
-            Next step : consider parameterized curve.  */
-
-        /* Get data on current patch */
-        int mx,my,mbc;
-        double xlower,ylower,dx,dy;    
-        fclaw_clawpatch_2d_grid_data(glob,patch,&mx,&my,&mbc,
-                                    &xlower,&ylower,&dx,&dy);
-
-        if (swirl_ray->rtype == SWIRL_RAY_LINE)
-        {
-            /* Check to see if line segment intersections one of four edges. */
-            point_t p0 = {swirl_ray->xy[0], swirl_ray->xy[1]};
-            point_t p1 = {p0.x + swirl_ray->r.line.vec[0],
-                          p0.y + swirl_ray->r.line.vec[1]};
-
-            double xupper = xlower + dx*mx;
-            double yupper = ylower + dy*my;
-            double qx[5] = {xlower, xupper, xupper, xlower, xlower};
-            double qy[5] = {ylower, ylower, yupper, yupper, ylower};
-
-            point_t r;
-            int istart = -1, iend = -1;
-            point_t r0, r1;        
-            /* Check intersection of ray with each edge of quadrant */
-            for(int i = 0; i < 4; i++)
-            {
-                point_t q0 = {qx[i],qy[i]};
-                point_t q1 = {qx[i+1],qy[i+1]};
-
-                int found = segment_intersect(p0,p1,q0,q1,&r);
-                if (found != 0)
-                {
-                    if (istart < 0)
-                    {
-                        istart = i;
-                        r0 = r;
-                    }
-                    else
-                    {
-                        iend = i;
-                        r1 = r;
-                        break;
-                    }
-                }
-            }
-            /* Four cases */
-            int found_intersection = 0;
-            point_t pstart, pend;
-            if (istart < 0 && iend < 0)
-            {
-                /* No intersection found */
-                //fclaw_global_essentialf("No intersection found\n");
-                *integral = 0;
-            }
-            else if (istart >= 0 && iend >= 0)
-            {
-                /* Ray enters and exits quad */
-                //fclaw_global_essentialf("Ray enters and exits quad\n");
-                pstart = r0;
-                pend = r1;
-                found_intersection = 1;
-            }
-            else
-            {
-                /* Ray starts or ends in quad */
-                point_t pll = {xlower,ylower};
-                point_t pur = {xupper, yupper};
-                if (point_in_quad(p0,pll,pur) != 0)
-                {
-                    pstart = p0;
-                    pend = r0;
-                }
-                else if (point_in_quad(p1,pll,pur) != 0)
-                {
-                    //fclaw_global_essentialf("Ray starts outside quad and enters\n");       
-                    pstart = r0;
-                    pend = p1;
-                }
-                found_intersection = 1;
-            }
-            if (found_intersection != 0)
-            {
-                /* This could be replaced by an integral along a curve in the patch */
-                *integral = distance(pstart,pend);
-                
-                if (0)
-                {
-                    printf("%5d %f\n",patchno,*integral);
-                    printf("pstart : %f %f\n",pstart.x,pstart.y);
-                    printf("pend   : %f %f\n",pend.x,pend.y);
-                    printf("\n");
-                }
-            }
-        }  /* end of ray type line */
-        return 1;
-    } 
-    else 
-    {
-        /* We are not at a leaf and the patch is an artificial patch containing all
-        * standard patch information except for the pointer to the next patch and
-        * user-data of any kind. Only the FCLAW2D_PATCH_CHILDID and the
-        * FCLAW2D_PATCH_ON_BLOCK_FACE_* flags are set.
-        * Based on this, we now can run a test to check if the ray and the patch
-        * intersect.
-        * We return 0 if we are certain that the ray does not intersect any
-        * descendant of this patch.
-        * We return 1 if the test concludes that the ray may intersect the patch.
-        * This test may be overinclusive / false positive to optimize for speed.
-        *
-        * The purpose of this test is to remove irrelevant ancestor
-        * patch-ray-combinations early on to avoid unnecessary computations.
-        * We do not need to assign to the integral value for ancestor patches. */
-
-        /* This is a dummy example.  Truly, implement a fast and over-inclusive test
-        * to see if this ray may possibly intersect the patch and return the answer. */
-        return 1;
-    }
-}
-
-
-static int nlines = 3;
-
-
-/* Virtual function for setting rays */
-static
-void swirl_allocate_and_define_rays(fclaw_global_t *glob, 
-                                    fclaw_ray_t** rays, 
-                                    int* num_rays)
-{
-    *num_rays = nlines;
-
-    /* We let the user allocate an array of rays, although what is inside the 
-       generic ray type is left opaque. This is destroy in matching FREE,
-       below. */
-
-    //*rays = (fclaw2d_ray_t*) FCLAW_ALLOC(fclaw2d_ray_t,*num_rays);
-    *rays = fclaw_ray_allocate_rays(*num_rays);
-    fclaw_ray_t *ray_vec = *rays;
-    for (int i = 0; i < nlines; ++i) 
-    {
-        //fclaw_global_essentialf("ray_initialize : Setting up ray %d : \n",i);
-        swirl_ray_t *sr = (swirl_ray_t*) FCLAW_ALLOC(swirl_ray_t,1);
-        sr->rtype = SWIRL_RAY_LINE;
-
-#if 0
-        sr->xy[0] = 0.;
-        sr->xy[1] = 0.;
-        sr->r.line.vec[0] = cos (i * M_PI / (nlines-1));
-        sr->r.line.vec[1] = sin (i * M_PI / (nlines-1));
-#else        
-        /* End points are on a semi-circle in x>0,y>0 quad */
-        FCLAW_ASSERT(nlines >= 2);
-        sr->xy[0] = 0; //-0.1;
-        sr->xy[1] = 0; //-0.1;
-        double R = 2.0;
-        double dth = M_PI/(2*nlines);
-        sr->r.line.vec[0] = R*cos ((i+0.5) * dth);
-        sr->r.line.vec[1] = R*sin ((i+0.5) * dth);
-#endif        
-
-        fclaw_ray_t *ray = &ray_vec[i];
-        int id = i + 1;
-        fclaw_ray_set_ray(ray,id, sr);
-    }
-}
-
-
-static
-void swirl_deallocate_rays(fclaw_global_t *glob, 
-                           fclaw_ray_t** rays, 
-                           int* num_rays)
-{
-    fclaw_ray_t *ray_vec = *rays;
-    for(int i = 0; i < *num_rays; i++)
-    {
-        /* Retrieve rays set above and deallocate them */
-        int id;
-        fclaw_ray_t *ray = &ray_vec[i];
-        swirl_ray_t *rs = (swirl_ray_t*) fclaw_ray_get_ray(ray,&id);
-        FCLAW_ASSERT(rs != NULL);
-        FCLAW_FREE(rs);
-        rs = NULL;
-    }
-    /* Match FCLAW_ALLOC, above */
-    *num_rays = fclaw_ray_deallocate_rays(rays);
-}
-
-void swirl_initialize_rays(fclaw_global_t* glob)
-{
-    /* Set up rays */
-    fclaw_ray_vtable_t* rays_vt = fclaw_ray_vt(glob); 
-
-    rays_vt->allocate_and_define = swirl_allocate_and_define_rays;
-    rays_vt->deallocate = swirl_deallocate_rays;
-
-    rays_vt->integrate = swirl_intersect_ray;
-}
-
-
diff --git a/applications/demo/2d/swirl_restart/swirl_user.cpp b/applications/demo/2d/swirl_restart/swirl_user.cpp
index e0379f623..527f4fe0f 100644
--- a/applications/demo/2d/swirl_restart/swirl_user.cpp
+++ b/applications/demo/2d/swirl_restart/swirl_user.cpp
@@ -48,8 +48,6 @@ void swirl_link_solvers(fclaw_global_t *glob)
     fclaw_vtable_t *vt = fclaw_vt(glob);
     vt->problem_setup = &swirl_problem_setup;  /* Version-independent */
     
-    swirl_initialize_rays(glob);
-
     const user_options_t* user = swirl_get_options(glob);
     if (user->claw_version == 4)
     {

From 7af2469d53f89de63e65188545249ea5ddf96fa6 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Fri, 19 Jul 2024 08:47:27 -0600
Subject: [PATCH 02/24] (cleanup) Remove unused variables

---
 src/solvers/fc2d_clawpack5/fortran_source/clawpack5_flux2.f   | 4 ++--
 src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2.f90 | 2 +-
 .../fc2d_clawpack5/fortran_source/clawpack5_step2_wrap.f      | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_flux2.f b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_flux2.f
index 977591d12..6074ea1fc 100644
--- a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_flux2.f
+++ b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_flux2.f
@@ -54,8 +54,8 @@ subroutine clawpack5_flux2(ixy,maxm,meqn,maux,mbc,mx,
 c        where A^* represents either A^- or A^+.
 c
 c
-      use clawpack5_amr_module, only : mwaves, mcapa, method, 
-     &       mthlim, use_fwaves
+      use clawpack5_amr_module, only : mwaves, method, mthlim, 
+     &       use_fwaves
       implicit none
 
       external rpn2, rpt2
diff --git a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2.f90 b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2.f90
index d3e043f75..f8560ef09 100644
--- a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2.f90
+++ b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2.f90
@@ -14,7 +14,7 @@ SUBROUTINE clawpack5_step2(maxm,meqn,maux,mbc,mx,my,qold,aux,dx,dy,dt, &
 !     Converted to f90 2012-1-04 (KTM)
 !
 
-    use clawpack5_amr_module, only : mwaves, mcapa, method,mthlim
+    use clawpack5_amr_module, only : mwaves, mcapa
 
 
     implicit none
diff --git a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2_wrap.f b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2_wrap.f
index 3507180b3..fc4ec2d8a 100644
--- a/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2_wrap.f
+++ b/src/solvers/fc2d_clawpack5/fortran_source/clawpack5_step2_wrap.f
@@ -9,7 +9,7 @@ subroutine clawpack5_step2_wrap(maxm, meqn, maux, mbc,
       external rpn2,rpt2, flux2
 
       integer maxm,meqn,maux,mbc,mcapa,mwaves,mx,my, mwork
-      integer maxmx, maxmy, level, ierror, use_fwaves
+      integer maxmx, maxmy, level, ierror
       integer method(7), mthlim(mwaves)
       integer block_corner_count(0:3)
 

From fd813463c9768e740328f2d46c5c00c5f8a17dc2 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 15:52:11 -0700
Subject: [PATCH 03/24] (elliptic/heat) Fix 'uninitialized variable' warnings

---
 .../elliptic/heat/fortran/heat_qexact.f90     | 22 ++++++++++++++-----
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/applications/elliptic/heat/fortran/heat_qexact.f90 b/applications/elliptic/heat/fortran/heat_qexact.f90
index 9f5c209e7..da3fcbf3f 100644
--- a/applications/elliptic/heat/fortran/heat_qexact.f90
+++ b/applications/elliptic/heat/fortran/heat_qexact.f90
@@ -70,6 +70,11 @@ SUBROUTINE heat_qexact_complete(x,y,q,qlap,grad,flag)
     double precision q1, qx1, qy1, qlap1, x0p,y0p
     integer id
 
+    q = 0
+    qx = 0
+    qy = 0
+    qlap = 0        
+
     if (example .eq. 0) then
         q = x
         qx = 1
@@ -125,15 +130,14 @@ SUBROUTINE heat_qexact_complete(x,y,q,qlap,grad,flag)
         endif
     elseif (example .eq. 4) then
         q = 0
-        qx = 0
-        qy = 0
-        qlap = 0
         do id = 1,m_polar
             x0p = x0_polar(id)
             y0p = y0_polar(id)
             r = sqrt((x-x0p)**2 + (y-y0p)**2)
             theta = atan2(y-y0p,x-x0p)        
             q1 = 1 - hsmooth(id,r,theta)
+            qlap1 = 0
+            qx1 = 0
             if (flag .ge. 1) then
                 !! Assume mapping is T(r,theta)
                 t1(1) = cos(theta)
@@ -152,9 +156,13 @@ SUBROUTINE heat_qexact_complete(x,y,q,qlap,grad,flag)
                 endif
             endif
             q = q + q1
-            qx = qx + qx1
-            qy = qy + qy1
-            qlap = qlap + qlap1
+            if (flag .ge. 1) then
+                qx = qx + qx1
+                qy = qy + qy1
+                if (flag .eq. 2) then
+                    qlap = qlap + qlap1
+                endif
+            endif
         enddo
     endif
     if (flag .ge. 1) then
@@ -185,6 +193,8 @@ subroutine heat_fort_beta(x,y,b,grad)
 
     DOUBLE PRECISION bx, by
 
+    bx = 0
+    by = 0
     if (beta_choice .eq. 0) then
         b = 1
         bx = 0

From 9fee8e8a0227701e3cf5cdaf3e88b84a003c32e4 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:18:04 -0700
Subject: [PATCH 04/24] (heat_phasefield) Fix compiler warnings about
 unitialized variables

---
 .../heat_phasefield/heat/fortran/heat_apply_bc.f90     | 10 ++++++++++
 .../heat_phasefield/heat/fortran/heat_eval_bc.f90      |  4 ++++
 2 files changed, 14 insertions(+)

diff --git a/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90 b/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
index e7f3f2b77..21b7d34c8 100644
--- a/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
+++ b/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
@@ -51,6 +51,10 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
             end do
         end do
 
+
+        !! Assume Dirichlet BCs to suppress compiler warnings.
+        a = 1
+        b = 0
         do iface = 0,3
             if (intersects_bc(iface) .ne. 0) then
                 idir = iface/2   !! direction : 0 or 1
@@ -99,6 +103,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'heat_apply_bc : ic, i1, ig may not be initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -125,6 +132,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'heat_apply_bc : jc, j1, jg may not be initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy
diff --git a/applications/elliptic/heat_phasefield/heat/fortran/heat_eval_bc.f90 b/applications/elliptic/heat_phasefield/heat/fortran/heat_eval_bc.f90
index ddbfc6354..64e59fe55 100644
--- a/applications/elliptic/heat_phasefield/heat/fortran/heat_eval_bc.f90
+++ b/applications/elliptic/heat_phasefield/heat/fortran/heat_eval_bc.f90
@@ -18,6 +18,10 @@ double precision function heat_fort_eval_bc(iface,t,x,y)
     qn = normals(iface,1)*grad(1) + normals(iface,2)*grad(2)
 
     !! bc_type is set in options .ini file as [multigrid] boundary_conditions
+
+    !! Assume Dirichlet conditions (to suppress compiler warnings)
+    a = 1
+    b = 0
     if (bctype(iface) .eq. 1) then
         a = 1
         b = 0

From 812ea2d1c565393a70e2f27d8b7e2132543e403b Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:29:46 -0700
Subject: [PATCH 05/24] (elliptic/heat) Fix compiler warnings

---
 .../elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90 b/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
index 21b7d34c8..dbe822529 100644
--- a/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
+++ b/applications/elliptic/heat_phasefield/heat/fortran/heat_apply_bc.f90
@@ -53,8 +53,6 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
 
 
         !! Assume Dirichlet BCs to suppress compiler warnings.
-        a = 1
-        b = 0
         do iface = 0,3
             if (intersects_bc(iface) .ne. 0) then
                 idir = iface/2   !! direction : 0 or 1
@@ -66,6 +64,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'heat_apply_bc : bctype(iface) is not valid'
+                    stop
                 endif
 
                 if (idir == 0) then

From 1976d17d55e380fe51be4a3a12ff31c5a30b0ff7 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:40:12 -0700
Subject: [PATCH 06/24] (elliptic/heat_phasefield) Fix compiler warnings

---
 .../phasefield/fortran/phasefield_apply_bc.f90           | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/applications/elliptic/heat_phasefield/phasefield/fortran/phasefield_apply_bc.f90 b/applications/elliptic/heat_phasefield/phasefield/fortran/phasefield_apply_bc.f90
index 5bfebd9c5..4df057335 100644
--- a/applications/elliptic/heat_phasefield/phasefield/fortran/phasefield_apply_bc.f90
+++ b/applications/elliptic/heat_phasefield/phasefield/fortran/phasefield_apply_bc.f90
@@ -67,6 +67,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'phasefield_apply_bc : bctype(iface) not valid'
+                    stop
                 endif
 
                 if (idir == 0) then
@@ -104,6 +107,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'phasefield_appy_bc: ic, i1, ig not initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -130,6 +136,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'phasefield_appy_bc: jc, j1, jg not initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy

From a660c5e37b42650d9fb7aab94114f4e5ea347be7 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:43:30 -0700
Subject: [PATCH 07/24] (elliptic/poisson) fix compiler warnings

---
 .../elliptic/poisson/fortran/poisson_qexact.f90  | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/applications/elliptic/poisson/fortran/poisson_qexact.f90 b/applications/elliptic/poisson/fortran/poisson_qexact.f90
index d6269f202..93fa444f1 100644
--- a/applications/elliptic/poisson/fortran/poisson_qexact.f90
+++ b/applications/elliptic/poisson/fortran/poisson_qexact.f90
@@ -79,6 +79,9 @@ SUBROUTINE poisson_qexact_complete(example,x,y,q,qlap,grad,flag)
     double precision q1, qx1, qy1, qlap1, x0p,y0p
     integer id
 
+    qlap = 0
+    qx = 0
+    qy = 0
     if (example .eq. 0) then
         q = x**2 + y**2
         qx = 2*x
@@ -161,9 +164,13 @@ SUBROUTINE poisson_qexact_complete(example,x,y,q,qlap,grad,flag)
                 endif
             endif
             q = q + q1
-            qx = qx + qx1
-            qy = qy + qy1
-            qlap = qlap + qlap1
+            if (flag .ge. 1) then
+                qx = qx + qx1
+                qy = qy + qy1
+                if (flag .eq. 2) then
+                    qlap = qlap + qlap1
+                endif
+            endif
         enddo
     endif
     if (flag .ge. 1) then
@@ -206,6 +213,9 @@ subroutine poisson_fort_beta(x,y,b,grad)
         b = 1 + x*y
         bx = y
         by = x
+    else
+        write(6,*) 'poisson_qexact : Invalid beta choice'
+        stop
     endif
 
     grad(1) = bx

From 126ae14ca8db1efb9de77f0fda85d119caf5f1a9 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:50:51 -0700
Subject: [PATCH 08/24] (elliptic/phasefield) Fix compiler warnings

---
 .../elliptic/phasefield/fortran/phasefield_apply_bc.f90  | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/applications/elliptic/phasefield/fortran/phasefield_apply_bc.f90 b/applications/elliptic/phasefield/fortran/phasefield_apply_bc.f90
index 5bfebd9c5..b0039dc2a 100644
--- a/applications/elliptic/phasefield/fortran/phasefield_apply_bc.f90
+++ b/applications/elliptic/phasefield/fortran/phasefield_apply_bc.f90
@@ -67,6 +67,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'phasefield_apply_bc : bctype(iface) is not valid'
+                    stop
                 endif
 
                 if (idir == 0) then
@@ -104,6 +107,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'phasefield_apply_bc : ic, i1, ig are not initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -130,6 +136,9 @@ subroutine phasefield_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'phasefield_apply_bc : jc, j1, jg are not initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy

From 2ec624d40adb86df9218893e1ebdd888415c259a Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 16:58:11 -0700
Subject: [PATCH 09/24] (elliptic/heat_phasefield) Fix compiler warnings

---
 .../heat_phasefield/heat/fortran/heat_qexact.f90 | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/applications/elliptic/heat_phasefield/heat/fortran/heat_qexact.f90 b/applications/elliptic/heat_phasefield/heat/fortran/heat_qexact.f90
index 9f5c209e7..899d11a69 100644
--- a/applications/elliptic/heat_phasefield/heat/fortran/heat_qexact.f90
+++ b/applications/elliptic/heat_phasefield/heat/fortran/heat_qexact.f90
@@ -70,6 +70,9 @@ SUBROUTINE heat_qexact_complete(x,y,q,qlap,grad,flag)
     double precision q1, qx1, qy1, qlap1, x0p,y0p
     integer id
 
+    qx = 0
+    qy = 0
+    qlap = 0
     if (example .eq. 0) then
         q = x
         qx = 1
@@ -152,9 +155,13 @@ SUBROUTINE heat_qexact_complete(x,y,q,qlap,grad,flag)
                 endif
             endif
             q = q + q1
-            qx = qx + qx1
-            qy = qy + qy1
-            qlap = qlap + qlap1
+            if (flag .eq. 1) then
+                qx = qx + qx1
+                qy = qy + qy1
+                if (flag .eq. 2) then
+                    qlap = qlap + qlap1
+                endif
+            endif
         enddo
     endif
     if (flag .ge. 1) then
@@ -197,6 +204,9 @@ subroutine heat_fort_beta(x,y,b,grad)
         b = 1 + x*y
         bx = y
         by = x
+    else
+        write(6,*) 'heat_fort_beta : beta choice is invalid'
+        stop
     endif
 
     grad(1) = bx

From 06ce290c9393a6f460d9a6334aeba7f1b1168543 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 17:23:35 -0700
Subject: [PATCH 10/24] (fc2d_thunderegg) Fix compiler warnings

---
 .../fort_4.6/thunderegg_apply_bc_default.f90             | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/solvers/fc2d_thunderegg/fort_4.6/thunderegg_apply_bc_default.f90 b/src/solvers/fc2d_thunderegg/fort_4.6/thunderegg_apply_bc_default.f90
index 18109fab1..0cb72c779 100644
--- a/src/solvers/fc2d_thunderegg/fort_4.6/thunderegg_apply_bc_default.f90
+++ b/src/solvers/fc2d_thunderegg/fort_4.6/thunderegg_apply_bc_default.f90
@@ -32,6 +32,9 @@ subroutine thunderegg_fort_apply_bc_default(blockno, mx, my,mbc,meqn,xlower,ylow
             elseif (bctype(iface) .eq. 2) then
                 a = 0
                 b = 1
+            else
+                write(6,*) 'thunderegg_apply_bc_default : bctype(iface) is not valid'
+                stop
             endif
 
             if (idir == 0) then
@@ -53,6 +56,9 @@ subroutine thunderegg_fort_apply_bc_default(blockno, mx, my,mbc,meqn,xlower,ylow
                 elseif (iface .eq. 1) then
                     i1 = mx+1
                     ig = mx+1
+                else
+                    write(6,*) 'thunderegg_fort_apply_bc_default : i1, ig not initialized'
+                    stop
                 endif
                 !! location at interface
                 x = xlower + (i1 - 1)*dx    
@@ -73,6 +79,9 @@ subroutine thunderegg_fort_apply_bc_default(blockno, mx, my,mbc,meqn,xlower,ylow
                 elseif (iface .eq. 3) then
                     j1 = my+1
                     jg = my+1
+                else
+                    write(6,*) 'thunderegg_fort_apply_bc_default : j1, jg not initialized'
+                    stop
                 endif
                 !! location at interface
                 y = ylower + (j1 - 1)*dy

From c109f1aa0a0b7f3acffb9fe3766785c2b2c0b18c Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 17:33:52 -0700
Subject: [PATCH 11/24] (clawpack/tranport/2d/all) Fix compiler warnings

---
 .../clawpack/transport/2d/all/clawpack46_rpt2cons_manifold.f    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/clawpack/transport/2d/all/clawpack46_rpt2cons_manifold.f b/applications/clawpack/transport/2d/all/clawpack46_rpt2cons_manifold.f
index 6a7119445..b3f5a1c01 100644
--- a/applications/clawpack/transport/2d/all/clawpack46_rpt2cons_manifold.f
+++ b/applications/clawpack/transport/2d/all/clawpack46_rpt2cons_manifold.f
@@ -5,7 +5,7 @@ subroutine clawpack46_rpt2cons_manifold(ixy,maxm,meqn,
       
       implicit none
 
-      integer ixy, maxm, meqn,mwaves,mbc,mx,imp, maux
+      integer ixy, maxm, meqn,mwaves,mbc,mx,imp
 
       double precision     ql(1-mbc:maxm+mbc, meqn)
       double precision     qr(1-mbc:maxm+mbc, meqn)

From 40cde8baad8d982e40f37cc47457c066f59137a4 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 17:38:13 -0700
Subject: [PATCH 12/24] (clawpack/euler/2d/quadrants) Fix compiler warnings

---
 .../clawpack/euler/2d/quadrants/user_4.6/qinit.f | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/applications/clawpack/euler/2d/quadrants/user_4.6/qinit.f b/applications/clawpack/euler/2d/quadrants/user_4.6/qinit.f
index f1cd66411..fe3f0591a 100644
--- a/applications/clawpack/euler/2d/quadrants/user_4.6/qinit.f
+++ b/applications/clawpack/euler/2d/quadrants/user_4.6/qinit.f
@@ -63,10 +63,18 @@ subroutine clawpack46_qinit(maxmx,maxmy,meqn,mbc,mx,my,
          xcell = xlower + (i-0.5d0)*dx
          do j = 1-mbc,my+mbc
             ycell = ylower + (j-0.5d0)*dy
-            if (xcell.ge.xs .and. ycell.ge.ys) iq = 1
-            if (xcell.lt.xs .and. ycell.ge.ys) iq = 2
-            if (xcell.lt.xs .and. ycell.lt.ys) iq = 3
-            if (xcell.ge.xs .and. ycell.lt.ys) iq = 4
+            if (xcell .ge. xs .and. ycell .ge. ys) then
+                  iq = 1
+            elseif (xcell .lt. xs .and. ycell .ge. ys) then
+                  iq = 2
+            elseif (xcell .lt. xs .and. ycell .lt. ys) then 
+                  iq = 3
+            elseif (xcell .ge. xs .and. ycell .lt. ys) then
+                  iq = 4
+            else
+                  write(6,*) "qinit.f : invalid point value"
+                  stop
+            endif
             q(i,j,1) = rpr(iq)
             q(i,j,2) = rpr(iq)*rpu(iq)
             q(i,j,3) = rpr(iq)*rpv(iq)

From c1182204a602e59233dbde3435d99343e3028b5d Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Sun, 21 Jul 2024 17:57:06 -0700
Subject: [PATCH 13/24] (clawpack/shallow/2d/sphere) Fix compiler warnings

---
 .../shallow/2d/sphere/user_4.6/rpn2swsphere_fwave.f90  | 10 ++++------
 .../shallow/2d/sphere/user_4.6/sphere_b4step2.f90      |  1 -
 .../shallow/2d/sphere/user_4.6/sphere_setaux.f90       |  2 +-
 .../clawpack/shallow/2d/sphere/user_5.0/rpt2swq.f90    |  5 ++---
 .../shallow/2d/sphere/user_5.0/rpt2swq_fwave.f90       |  5 ++---
 5 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/applications/clawpack/shallow/2d/sphere/user_4.6/rpn2swsphere_fwave.f90 b/applications/clawpack/shallow/2d/sphere/user_4.6/rpn2swsphere_fwave.f90
index 45d21745c..308d0f01c 100644
--- a/applications/clawpack/shallow/2d/sphere/user_4.6/rpn2swsphere_fwave.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_4.6/rpn2swsphere_fwave.f90
@@ -42,14 +42,12 @@ SUBROUTINE clawpack46_rpn2_fwave(ixy,maxm,meqn,mwaves, &
 
     integer :: i, m, mw, mq, ioff
     double precision :: enx, eny, enz, etx,ety,etz
-    double precision :: hunl, hunr, hutl, hutr
-    double precision :: gamma, amn, apn, df, dy, qn
+    double precision :: hunl, hunr
+    double precision :: gamma, amn, apn, df, dy
     double precision :: erx, ery, erz, h1, h3, hi, him1, hu1, hu3
     double precision :: s0, s03, s1, s3, sfract
 
     double precision :: hL, hR, huL, huR, bL, bR, hvL, hvR
-    double precision :: uL, vL, uR, vR, phiR, phiL, sL, sR
-    double precision :: uhat, chat
     double precision :: sw(mwaves), fw(meqn,mwaves)
     double precision szm(3), szp(3), z, sdk
 
@@ -327,8 +325,8 @@ SUBROUTINE simple_riemann(hR,huR,hvR, br, hL,huL,hvl,bL, s,fwave)
     common /swe_model_parms/  grav
 
     DOUBLE PRECISION :: fluxdiff(3),beta(3), hbar, fl(3), fr(3)
-    double precision :: psiL, psiR, sL, sR, vhat, ul, vl, ur, vr
-    double precision :: hsq, uhat, chat, phir, phil
+    double precision :: psiL, psiR, vhat, ul, vl, ur, vr
+    double precision :: uhat,chat
 
     fwave = 0
     s = 0
diff --git a/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_b4step2.f90 b/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_b4step2.f90
index d5f85ad8a..ee003b6f9 100644
--- a/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_b4step2.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_b4step2.f90
@@ -8,7 +8,6 @@ subroutine clawpack46_b4step2(maxmx,maxmy,mbc,mx,my,meqn,q, &
    double precision  q(1-mbc:maxmx+mbc,1-mbc:maxmy+mbc, meqn)
    double precision aux(1-mbc:maxmx+mbc,1-mbc:maxmy+mbc, maux)
 
-   double precision xlow,ylow
    double precision erx, ery, erz, qn
 
    integer i,j
diff --git a/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_setaux.f90 b/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_setaux.f90
index aef2844a5..a6ced9ec8 100644
--- a/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_setaux.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_4.6/sphere_setaux.f90
@@ -25,7 +25,7 @@ subroutine sphere_setaux(mx,my,mbc,xlower,ylower, &
     common /swe_example/ example
 
    integer i,j,m
-   double precision dxdy, xc, yc, xp, yp,zp, rp
+   double precision dxdy, xc, yc
    double precision bmount
 
    integer blockno, fc2d_clawpack46_get_block
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq.f90
index 1900fa04b..52606cba9 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq.f90
@@ -37,9 +37,8 @@ subroutine clawpack5_rpt2(ixy,imp,maxm,meqn,mwaves,maux, &
     common /comxyt/ dtcom,dxcom,dycom,tcom,icom,jcom
 
     double precision delta(4)
-    double precision a1, a2, a3, dx, dy, bn
-    double precision erx, ery, erz 
-    integer i, j, m, i1, mw, ioff, ix1, ixm1
+    double precision a1, a2, a3, dx
+    integer i, m, i1, mw, ioff, ix1, ixm1
 
 
     if (ixy .eq. 1) then
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq_fwave.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq_fwave.f90
index bae234972..e344ae838 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq_fwave.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/rpt2swq_fwave.f90
@@ -37,9 +37,8 @@ subroutine clawpack5_rpt2_fwave(ixy,imp,maxm,meqn,mwaves, maux,&
     common /comxyt/ dtcom,dxcom,dycom,tcom,icom,jcom
 
     double precision delta(4)
-    double precision a1, a2, a3, dx, dy, bn
-    double precision erx, ery, erz 
-    integer i, j, m, i1, mw, ioff, ix1, ixm1
+    double precision a1, a2, a3, dx
+    integer i, m, i1, mw, ioff, ix1, ixm1
 
 
     if (ixy .eq. 1) then

From fbf1cef7746e88ac4f675683c0f93e218b1066b9 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 12:53:57 -0700
Subject: [PATCH 14/24] (elliptic/allencahn) Fix compiler warnings

---
 .../allencahn/fortran/allencahn_apply_bc.f90  |  9 ++++++++
 .../allencahn/fortran/allencahn_eval_bc.f90   |  3 +++
 .../allencahn/fortran/allencahn_qexact.f90    | 22 ++++++++++++++-----
 3 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/applications/elliptic/allencahn/fortran/allencahn_apply_bc.f90 b/applications/elliptic/allencahn/fortran/allencahn_apply_bc.f90
index 57e044d11..e8f422bd7 100644
--- a/applications/elliptic/allencahn/fortran/allencahn_apply_bc.f90
+++ b/applications/elliptic/allencahn/fortran/allencahn_apply_bc.f90
@@ -80,6 +80,9 @@ subroutine allencahn_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'allencahn_apply_bc : Invalid bctype choice'
+                    stop
                 endif
 
                 if (idir == 0) then
@@ -117,6 +120,9 @@ subroutine allencahn_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'allencahn_apply_bc : ic, i1, ig not initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -143,6 +149,9 @@ subroutine allencahn_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'allencahn_apply_bc : jc, j1, jg not initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy
diff --git a/applications/elliptic/allencahn/fortran/allencahn_eval_bc.f90 b/applications/elliptic/allencahn/fortran/allencahn_eval_bc.f90
index 834e48ef3..2b0add3a8 100644
--- a/applications/elliptic/allencahn/fortran/allencahn_eval_bc.f90
+++ b/applications/elliptic/allencahn/fortran/allencahn_eval_bc.f90
@@ -24,6 +24,9 @@ double precision function allencahn_fort_eval_bc(iface,t,x,y)
     elseif (bctype(iface) .eq. 2) then
         a = 0
         b = 1
+    else
+        write(6,*) 'allencahn_eval_bc : Invalid bctype'
+        stop
     endif
 
     allencahn_fort_eval_bc = a*q + b*qn
diff --git a/applications/elliptic/allencahn/fortran/allencahn_qexact.f90 b/applications/elliptic/allencahn/fortran/allencahn_qexact.f90
index d35f3e0b2..5bea9d520 100644
--- a/applications/elliptic/allencahn/fortran/allencahn_qexact.f90
+++ b/applications/elliptic/allencahn/fortran/allencahn_qexact.f90
@@ -70,6 +70,8 @@ SUBROUTINE allencahn_qexact_complete(x,y,q,qlap,grad,flag)
     double precision q1, qx1, qy1, qlap1, x0p,y0p
     integer id
 
+    qx = 0
+    qy = 0
     if (example .eq. 0) then
         q = x**2 + y**2
         qx = 2*x
@@ -127,13 +129,13 @@ SUBROUTINE allencahn_qexact_complete(x,y,q,qlap,grad,flag)
         q = 0
         qx = 0
         qy = 0
-        qlap = 0
+        qlap = 0        
         do id = 1,m_polar
             x0p = x0_polar(id)
             y0p = y0_polar(id)
             r = sqrt((x-x0p)**2 + (y-y0p)**2)
             theta = atan2(y-y0p,x-x0p)        
-            q1 = 1 - hsmooth(id,r,theta)
+            q1 = 1 - hsmooth(id,r,theta)            
             if (flag .ge. 1) then
                 !! Assume mapping is T(r,theta)
                 t1(1) = cos(theta)
@@ -152,10 +154,17 @@ SUBROUTINE allencahn_qexact_complete(x,y,q,qlap,grad,flag)
                 endif
             endif
             q = q + q1
-            qx = qx + qx1
-            qy = qy + qy1
-            qlap = qlap + qlap1
+            if (flag .ge. 1) then
+                qx = qx + qx1
+                qy = qy + qy1
+                if (flag .eq. 2) then
+                    qlap = qlap + qlap1
+                endif
+            endif
         enddo
+    else
+        write(6,*) 'allencahn_qexact : Invalid example choice'
+        stop
     endif
     if (flag .ge. 1) then
         grad(1) = qx
@@ -197,6 +206,9 @@ subroutine allencahn_fort_beta(x,y,b,grad)
         b = 1 + x*y
         bx = y
         by = x
+    else
+        write(6,*) 'allencahn_beta : Invalid beta choice'
+        stop
     endif
 
     grad(1) = bx

From cecb7cff22fdad8eb8b0920efc0cd20dac28f585 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 12:57:08 -0700
Subject: [PATCH 15/24] (elliptic/heat) Fix compiler warnings

---
 applications/elliptic/heat/fortran/heat_apply_bc.f90 | 9 +++++++++
 applications/elliptic/heat/fortran/heat_eval_bc.f90  | 3 +++
 2 files changed, 12 insertions(+)

diff --git a/applications/elliptic/heat/fortran/heat_apply_bc.f90 b/applications/elliptic/heat/fortran/heat_apply_bc.f90
index e7f3f2b77..4b97db29c 100644
--- a/applications/elliptic/heat/fortran/heat_apply_bc.f90
+++ b/applications/elliptic/heat/fortran/heat_apply_bc.f90
@@ -62,6 +62,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'heat_apply_bc : Invalid bctype'
+                    stop
                 endif
 
                 if (idir == 0) then
@@ -99,6 +102,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'heat_apply_bc : ic, i1, or ig not initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -125,6 +131,9 @@ subroutine heat_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'heat_apply_bc : jc, j1, or jg not initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy
diff --git a/applications/elliptic/heat/fortran/heat_eval_bc.f90 b/applications/elliptic/heat/fortran/heat_eval_bc.f90
index ddbfc6354..681203f4e 100644
--- a/applications/elliptic/heat/fortran/heat_eval_bc.f90
+++ b/applications/elliptic/heat/fortran/heat_eval_bc.f90
@@ -24,6 +24,9 @@ double precision function heat_fort_eval_bc(iface,t,x,y)
     elseif (bctype(iface) .eq. 2) then
         a = 0
         b = 1
+    else
+        write(6,*) 'heat_eval_bc : Invalid bctype'
+        stop
     endif
 
     heat_fort_eval_bc = a*q + b*qn

From c8efd6847ea21ee325842c6d4fb40a2569f5e2f2 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 13:23:53 -0700
Subject: [PATCH 16/24] (elliptic/poisson) Fix compiler warnings

---
 .../elliptic/poisson/fortran/poisson_apply_bc.f90        | 9 +++++++++
 .../elliptic/poisson/fortran/poisson_eval_bc.f90         | 3 +++
 2 files changed, 12 insertions(+)

diff --git a/applications/elliptic/poisson/fortran/poisson_apply_bc.f90 b/applications/elliptic/poisson/fortran/poisson_apply_bc.f90
index 9e9c4ddf9..e5a20437e 100644
--- a/applications/elliptic/poisson/fortran/poisson_apply_bc.f90
+++ b/applications/elliptic/poisson/fortran/poisson_apply_bc.f90
@@ -80,6 +80,9 @@ subroutine poisson_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                 elseif (bctype(iface) .eq. 2) then
                     a = 0
                     b = 1
+                else
+                    write(6,*) 'poisson_apply_bc : Invalid bctype choice'
+                    stop
                 endif
 
                 if (idir == 0) then
@@ -117,6 +120,9 @@ subroutine poisson_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         ic = mx  !! cell center
                         i1 = mx+1
                         ig = mx+1
+                    else
+                        write(6,*) 'poisson_apply_bc : ic, i1, or ig not initialized'
+                        stop
                     endif
                     !! location at interface
                     x = xlower + (i1 - 1)*dx    
@@ -143,6 +149,9 @@ subroutine poisson_fort_apply_bc(blockno, mx, my,mbc,mfields,xlower,ylower, &
                         jc = my
                         j1 = my+1
                         jg = my+1
+                    else
+                        write(6,*) 'poisson_apply_bc : jc, j1, or jg not initialized'
+                        stop
                     endif
                     !! location at interface
                     y = ylower + (j1 - 1)*dy
diff --git a/applications/elliptic/poisson/fortran/poisson_eval_bc.f90 b/applications/elliptic/poisson/fortran/poisson_eval_bc.f90
index d0fa80057..579afeb83 100644
--- a/applications/elliptic/poisson/fortran/poisson_eval_bc.f90
+++ b/applications/elliptic/poisson/fortran/poisson_eval_bc.f90
@@ -24,6 +24,9 @@ double precision function poisson_fort_eval_bc(iface,t,x,y)
     elseif (bctype(iface) .eq. 2) then
         a = 0
         b = 1
+    else
+        write(6,*) 'poisson_eval_bc : Invalid choice for bctype'
+        stop
     endif
 
     poisson_fort_eval_bc = a*q + b*qn

From 2a24459952905e224849847fb0ab7c8bb9d07c35 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 13:40:36 -0700
Subject: [PATCH 17/24] (fc3d_clawpack46) Fix compiler warnings

---
 .../fortran_source/fc3d_clawpack46_step3_wrap.f90             | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/solvers/fc3d_clawpack46/fortran_source/fc3d_clawpack46_step3_wrap.f90 b/src/solvers/fc3d_clawpack46/fortran_source/fc3d_clawpack46_step3_wrap.f90
index 482c01784..81e23d460 100644
--- a/src/solvers/fc3d_clawpack46/fortran_source/fc3d_clawpack46_step3_wrap.f90
+++ b/src/solvers/fc3d_clawpack46/fortran_source/fc3d_clawpack46_step3_wrap.f90
@@ -40,10 +40,6 @@ subroutine clawpack46_step3_wrap(maxm, meqn, maux, mbc, &
     double precision :: dtcom, dxcom,dycom,dzcom, tcom
     integer :: icom, jcom, kcom
     common /comxyzt/ dtcom,dxcom,dycom,dzcom, tcom,icom,jcom, kcom
-
-    integer jfix, kfix
-    double precision kappa
-
     ierror = 0
 
     !! This should be set to actual time, in case the user wants it

From 4688825e1700bfbe033226007ce399da381cc42f Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 14:04:02 -0700
Subject: [PATCH 18/24] (clawpatch/fort3_4.6) Fix compiler warnings

---
 src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_copy.f90  | 2 --
 .../clawpatch/fort3_4.6/fclaw3d_clawpatch46_interpolate.f90   | 4 ----
 .../clawpatch/fort3_4.6/fclaw3dx_clawpatch46_average.f90      | 3 +--
 3 files changed, 1 insertion(+), 8 deletions(-)

diff --git a/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_copy.f90 b/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_copy.f90
index 37c8cc113..672e2c7ed 100644
--- a/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_copy.f90
+++ b/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_copy.f90
@@ -22,8 +22,6 @@ subroutine fclaw3d_clawpatch46_fort_copy_face(mx,my,mz,mbc, &
     integer mq, k
     integer i,j
 
-    integer a(2,2), f(2)
-
     !!call fclaw3d_clawpatch_build_transform_same(transform_ptr, a, f)
 
     if (iface .eq. 0) then
diff --git a/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_interpolate.f90 b/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_interpolate.f90
index 0d1c33fdf..51e118973 100644
--- a/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_interpolate.f90
+++ b/src/patches/clawpatch/fort3_4.6/fclaw3d_clawpatch46_interpolate.f90
@@ -46,7 +46,6 @@ subroutine fclaw3d_clawpatch46_fort_interpolate_face &
     integer :: rr3
     parameter(rr3 = 8)
     integer :: i2(0:rr3-1),j2(0:rr3-1),k2(0:rr3-1)
-    logical :: fclaw3d_clawpatch_is_valid_interp
     logical :: skip_this_grid
 
     integer :: a(3,3), f(3)
@@ -385,12 +384,9 @@ subroutine fclaw3d_clawpatch46_fort_interpolate2fine &
 
     integer :: ii, jj, kk, i,j,k, i1, i2, j1, j2, k1, k2, ig, jg, kg, mq, mth
     integer :: ic,jc,kc,ic_add, jc_add, kc_add, ifine, jfine, kfine
-    integer :: i_start_fine, j_start_fine, k_start_fine
     double precision :: qc, shiftx, shifty, shiftz, sl, sr, gradx, grady, gradz
     double precision :: fclaw2d_clawpatch_compute_slopes
 
-    logical :: lower_x, lower_y, lower_z
-
     integer :: p8est_refineFactor,refratio
 
     p8est_refineFactor = 2
diff --git a/src/patches/clawpatch/fort3_4.6/fclaw3dx_clawpatch46_average.f90 b/src/patches/clawpatch/fort3_4.6/fclaw3dx_clawpatch46_average.f90
index 7782a4368..c48cfb178 100644
--- a/src/patches/clawpatch/fort3_4.6/fclaw3dx_clawpatch46_average.f90
+++ b/src/patches/clawpatch/fort3_4.6/fclaw3dx_clawpatch46_average.f90
@@ -50,7 +50,6 @@ SUBROUTINE fclaw3dx_clawpatch46_fort_average_face(mx,my,mz,mbc,meqn, &
     INTEGER :: rr2
     PARAMETER(rr2 = 4)
     INTEGER, DIMENSION(0:rr2-1) :: i2, j2
-    !! DOUBLE PRECISION :: kc
 
     LOGICAL :: fclaw2d_clawpatch_is_valid_average, skip_this_grid
     DOUBLE PRECISION :: vf_sum
@@ -192,7 +191,7 @@ subroutine fclaw3dx_clawpatch46_fort_average_corner(mx,my,mz,mbc,meqn, &
     INTEGER :: i2(0:rr2-1),j2(0:rr2-1)
 
     INTEGER :: i1,j1,m, k
-    DOUBLE PRECISION :: vf_sum, kc
+    DOUBLE PRECISION :: vf_sum
 
     r2 = refratio*refratio
     if (r2 .ne. rr2) then

From cdc1fea06c63595e8340da4585ef83bdce93d297 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 14:23:26 -0700
Subject: [PATCH 19/24] (clawpack/shallow/sphere) Fix compiler warnings

---
 .../clawpack/shallow/2d/sphere/user_4.6/rpt2swq.f90         | 5 ++---
 .../clawpack/shallow/2d/sphere/user_4.6/rpt2swq_fwave.f90   | 5 ++---
 .../clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere.f90    | 2 +-
 .../shallow/2d/sphere/user_5.0/rpn2swsphere_fwave.f90       | 6 ++----
 .../clawpack/shallow/2d/sphere/user_5.0/sphere_b4step2.f90  | 5 -----
 .../clawpack/shallow/2d/sphere/user_5.0/sphere_qinit.f90    | 4 +---
 .../clawpack/shallow/2d/sphere/user_5.0/sphere_setaux.f90   | 2 +-
 7 files changed, 9 insertions(+), 20 deletions(-)

diff --git a/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq.f90 b/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq.f90
index fa570cbb2..c49f0d885 100644
--- a/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq.f90
@@ -37,9 +37,8 @@ subroutine clawpack46_rpt2(ixy,maxm,meqn,mwaves,mbc,mx, &
     common /comxyt/ dtcom,dxcom,dycom,tcom,icom,jcom
 
     double precision delta(4)
-    double precision a1, a2, a3, dx, dy, bn
-    double precision erx, ery, erz 
-    integer i, j, m, i1, mw, ioff, ix1, ixm1
+    double precision a1, a2, a3, dx
+    integer i, m, i1, mw, ioff, ix1, ixm1
 
 
     if (ixy .eq. 1) then
diff --git a/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq_fwave.f90 b/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq_fwave.f90
index d94b7341a..903b19ba1 100644
--- a/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq_fwave.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_4.6/rpt2swq_fwave.f90
@@ -40,9 +40,8 @@ subroutine clawpack46_rpt2_fwave(ixy,maxm,meqn,mwaves,mbc,mx, &
     common /comxyt/ dtcom,dxcom,dycom,tcom,icom,jcom
 
     double precision delta(4)
-    double precision a1, a2, a3, dx, dy, bn
-    double precision erx, ery, erz 
-    integer i, j, m, i1, mw, ioff, ix1, ixm1
+    double precision a1, a2, a3, dx
+    integer i, m, i1, mw, ioff, ix1, ixm1
 
 
     if (ixy .eq. 1) then
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere.f90
index bd89391d2..608dcb8b5 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere.f90
@@ -27,7 +27,7 @@ subroutine clawpack5_rpn2(ixy,maxm,meqn,mwaves,maux, mbc,mx,&
     double precision amn, erx, ery, erz, apn
     integer ioff, m, mw, i
 
-    double precision dx, dy, qn
+    double precision dx, dy
 
 
     double precision grav
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere_fwave.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere_fwave.f90
index d545c4548..71d9bb375 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere_fwave.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/rpn2swsphere_fwave.f90
@@ -42,14 +42,12 @@ SUBROUTINE clawpack5_rpn2_fwave(ixy,maxm,meqn,mwaves, maux, &
 
     integer :: i, m, mw, mq, ioff
     double precision :: enx, eny, enz, etx,ety,etz
-    double precision :: hunl, hunr, hutl, hutr
-    double precision :: gamma, amn, apn, df, dy, qn
+    double precision :: hunl, hunr
+    double precision :: gamma, amn, apn, df, dy
     double precision :: erx, ery, erz, h1, h3, hi, him1, hu1, hu3
     double precision :: s0, s03, s1, s3, sfract
 
     double precision :: hL, hR, huL, huR, bL, bR, hvL, hvR
-    double precision :: uL, vL, uR, vR, phiR, phiL, sL, sR
-    double precision :: uhat, chat
     double precision :: sw(mwaves), fw(meqn,mwaves)
     double precision szm(3), szp(3), z, sdk
 
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_b4step2.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_b4step2.f90
index 8dcc40e2e..f425ab313 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_b4step2.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_b4step2.f90
@@ -8,15 +8,10 @@ subroutine clawpack5_b4step2(mbc,mx,my,meqn,q, &
    double precision   q(meqn,1-mbc:mx+mbc,1-mbc:my+mbc)
    double precision aux(maux,1-mbc:mx+mbc,1-mbc:my+mbc)
 
-   double precision xlow,ylow
    double precision erx, ery, erz, qn
 
    integer i,j
 
-   !! # We may not even need this if we project out the correct surface
-   !! # normal from the velocities.
-   return
-
    do i=1,mx
       do j=1,my
          !! Surface normal
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_qinit.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_qinit.f90
index e1b5a8ad5..b3b231588 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_qinit.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_qinit.f90
@@ -33,13 +33,11 @@ subroutine clawpack5_qinit(meqn,mbc,mx,my, &
     double precision xc,yc,xlow,ylow,xp,yp,zp, w, qval
 
     double precision phi, phi0, width
-    double precision theta, q1, R, u0, Rsphere, d
+    double precision theta, q1, R, u0, d
 
     integer blockno, fc2d_clawpack5_get_block
     integer*8 cont, fclaw_map_get_context
 
-    character(len=12) :: fname
-
 
     cont = fclaw_map_get_context()
 
diff --git a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_setaux.f90 b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_setaux.f90
index 186e53a4f..187b1f160 100644
--- a/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_setaux.f90
+++ b/applications/clawpack/shallow/2d/sphere/user_5.0/sphere_setaux.f90
@@ -25,7 +25,7 @@ subroutine sphere5_setaux(mx,my,mbc,xlower,ylower, &
     common /swe_example/ example
 
    integer i,j,m
-   double precision dxdy, xc, yc, xp, yp,zp, rp
+   double precision dxdy, xc, yc
    double precision bmount
 
    integer blockno, fc2d_clawpack5_get_block

From 815aae43f11c2bf99483dbb3ba849980080530a4 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 14:33:13 -0700
Subject: [PATCH 20/24] (clawpack/euler/quadrants) Fix compiler warnings

---
 .../euler/2d/quadrants/user_5.0/qinit.f90        | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/applications/clawpack/euler/2d/quadrants/user_5.0/qinit.f90 b/applications/clawpack/euler/2d/quadrants/user_5.0/qinit.f90
index 4c65326cd..0c5e50167 100644
--- a/applications/clawpack/euler/2d/quadrants/user_5.0/qinit.f90
+++ b/applications/clawpack/euler/2d/quadrants/user_5.0/qinit.f90
@@ -54,10 +54,18 @@ SUBROUTINE clawpack5_qinit(meqn,mbc,mx,my, &
      xcell = xlower + (i-0.5d0)*dx
      DO j = 1-mbc,my+mbc
         ycell = ylower + (j-0.5d0)*dy
-        IF (xcell.GE.xs .AND. ycell.GE.ys) iq = 1
-        IF (xcell.LT.xs .AND. ycell.GE.ys) iq = 2
-        IF (xcell.LT.xs .AND. ycell.LT.ys) iq = 3
-        IF (xcell.GE.xs .AND. ycell.LT.ys) iq = 4
+        IF (xcell.GE.xs .AND. ycell.GE.ys) then
+            iq = 1        
+        ELSEIF (xcell.LT.xs .AND. ycell.GE.ys) then 
+            iq = 2
+        ELSEIF (xcell.LT.xs .AND. ycell.LT.ys) then 
+            iq = 3
+        ELSEIF (xcell.GE.xs .AND. ycell.LT.ys) then 
+            iq = 4
+        ELSE
+            write(6,*) 'qinit : (xs,ys) not in domain'
+            stop
+        ENDIF
         q(1,i,j) = rpr(iq)
         q(2,i,j) = rpr(iq)*rpu(iq)
         q(3,i,j) = rpr(iq)*rpv(iq)

From e08232fbed26195fd0ddd47eb01d843fee0558e3 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 14:44:11 -0700
Subject: [PATCH 21/24] (euler/3dx/rp) Fix compiler warnings

---
 .../clawpack/euler/3dx/rp/rpn3_euler.f90       |  4 ----
 .../euler/3dx/rp/rpn3_euler_mapped.f90         | 14 --------------
 .../euler/3dx/rp/rpt3_euler_mapped.f90         |  3 ---
 .../euler/3dx/rp/rptt3_euler_mapped.f90        | 18 +-----------------
 4 files changed, 1 insertion(+), 38 deletions(-)

diff --git a/applications/clawpack/euler/3dx/rp/rpn3_euler.f90 b/applications/clawpack/euler/3dx/rp/rpn3_euler.f90
index 82d22009c..c39731aa7 100644
--- a/applications/clawpack/euler/3dx/rp/rpn3_euler.f90
+++ b/applications/clawpack/euler/3dx/rp/rpn3_euler.f90
@@ -322,8 +322,4 @@ SUBROUTINE clawpack46_rpn3(ixyz,maxm,meqn,mwaves,maux,mbc,mx,ql,qr,  &
 
     END IF ! Entropy fix
 
-108     format(A,'ixyz=',I2, ';  imp = ',I2, ';  i = ', I2)
-109     format(5E24.16)
-
-
 END SUBROUTINE clawpack46_rpn3
diff --git a/applications/clawpack/euler/3dx/rp/rpn3_euler_mapped.f90 b/applications/clawpack/euler/3dx/rp/rpn3_euler_mapped.f90
index b0ff49c0c..3ea8a840b 100644
--- a/applications/clawpack/euler/3dx/rp/rpn3_euler_mapped.f90
+++ b/applications/clawpack/euler/3dx/rp/rpn3_euler_mapped.f90
@@ -312,22 +312,8 @@ subroutine clawpack46_rpn3_mapped(ixyz,maxm,meqn,mwaves,maux,mbc,mx,&
             apdq_cart(m,i) = area*apdq(m)
             amdq_cart(m,i) = area*amdq(m)
         end do
-
-
-!!        do m=1,meqn
-!!            amdq_cart(m,i) = 0.d0
-!!            apdq_cart(m,i) = 0.d0
-!!            do  mws = 1,mwaves
-!!                amdq_cart(m,i) = amdq_cart(m,i) + min(s(mws,i),0.d0)*wave(m,mws)
-!!                apdq_cart(m,i) = apdq_cart(m,i) + max(s(mws,i),0.d0)*wave(m,mws)
-!!            enddo
-!!        enddo
-
     enddo  !! end of i loop over 1d sweep array
 
-108     format(A,'ixyz=',I2,'; i = ',I2)
-109     format(5E24.16)
-
     return
 end subroutine clawpack46_rpn3_mapped
 
diff --git a/applications/clawpack/euler/3dx/rp/rpt3_euler_mapped.f90 b/applications/clawpack/euler/3dx/rp/rpt3_euler_mapped.f90
index 9f1cf43ec..257dc9381 100644
--- a/applications/clawpack/euler/3dx/rp/rpt3_euler_mapped.f90
+++ b/applications/clawpack/euler/3dx/rp/rpt3_euler_mapped.f90
@@ -243,9 +243,6 @@ subroutine clawpack46_rpt3_mapped(ixyz,icoor,ilr,maxm,meqn,mwaves,maux,mbc, &
 
     enddo  !! end of i loop
 
-108     format(A,'ixyz=',I2,'; icoor=',I2,'; ilr = ',I2,';  i=',I2)
-109     format(5E24.16)
-
 1001    format(A,3E24.16)
 1002    format(A,I5)
 1003    format('icom = ',I5,'; jcom = ',I5,'; kcom = ',I5)
diff --git a/applications/clawpack/euler/3dx/rp/rptt3_euler_mapped.f90 b/applications/clawpack/euler/3dx/rp/rptt3_euler_mapped.f90
index e0344d926..91402fd57 100644
--- a/applications/clawpack/euler/3dx/rp/rptt3_euler_mapped.f90
+++ b/applications/clawpack/euler/3dx/rp/rptt3_euler_mapped.f90
@@ -81,28 +81,12 @@ subroutine clawpack46_rptt3_mapped(ixyz,icoor,ilr,impt,maxm,meqn,mwaves,&
     common /comxyzt/ dtcom,dxcom,dycom,dzcom,tcom,icom,jcom,kcom
 
     double precision wave(5,3),s_rot(3), bsasdq(5), uvw(3)
-    double precision uvw_cart(3), rot(9), wave_cart(5,3)
+    double precision uvw_cart(3), rot(9)
 
     integer i, j, mws, m, i1, info
     double precision uvw2, pres, enth, area
     integer locrot, locarea, irot
 
-!!    integer mv,mu,mw
-
-!!    IF(ixyz == 1)THEN
-!!       mu = 2
-!!       mv = 3
-!!       mw = 4
-!!    ELSE IF(ixyz == 2)THEN
-!!       mu = 3
-!!       mv = 4
-!!       mw = 2
-!!    ELSE
-!!       mu = 4
-!!       mv = 2
-!!       mw = 3
-!!    ENDIF
-
     call get_aux_locations_tt(ixyz,icoor,mcapa,locrot,locarea,irot)
 
     !! # Solve Riemann problem in the second coordinate direction

From 0f1e2c155477ecfa5d76735946dcc955bb26648a Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 15:20:07 -0700
Subject: [PATCH 22/24] Fix compiler warnings

---
 src/fclaw_corner_neighbors.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/fclaw_corner_neighbors.c b/src/fclaw_corner_neighbors.c
index f127efedb..66da53adc 100644
--- a/src/fclaw_corner_neighbors.c
+++ b/src/fclaw_corner_neighbors.c
@@ -92,6 +92,9 @@ int find_edge(int corner, int intersects[], int faces[])
             face_0 = faces[0];
             face_1 = faces[1];
             break;
+        default:
+            fclaw_global_essentialf("fclaw_corner_neighbors : face_X not initialized");
+            exit(0);
     }
     FCLAW_ASSERT(face_0 != non_intersecting_face);
     FCLAW_ASSERT(face_1 != non_intersecting_face);

From 86801978aef9246912385bd11642e4f8191c8ed3 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 15:27:28 -0700
Subject: [PATCH 23/24] (demo) Fix compiler warnings

---
 .../clawpack/advection/2d/swirl/swirl_ray.c   |   5 +-
 .../filament_swirl/filament_swirl_split.cpp   |   4 +-
 .../demo/2d/filament_swirl/user_run.c         | 206 +-----------------
 3 files changed, 6 insertions(+), 209 deletions(-)

diff --git a/applications/clawpack/advection/2d/swirl/swirl_ray.c b/applications/clawpack/advection/2d/swirl/swirl_ray.c
index 872b698cf..03e81aa5a 100644
--- a/applications/clawpack/advection/2d/swirl/swirl_ray.c
+++ b/applications/clawpack/advection/2d/swirl/swirl_ray.c
@@ -1,5 +1,5 @@
 /*
-  Copyright (c) 2012-2022 Carsten Burstedde, Donna Calhoun, Scott Aiton
+  Copyright (c) 2012-2024 Carsten Burstedde, Donna Calhoun, Scott Aiton
   All rights reserved.
 
   Redistribution and use in source and binary forms, with or without
@@ -218,7 +218,8 @@ int swirl_intersect_ray (fclaw_domain_t *domain,
             }
             /* Four cases */
             int found_intersection = 0;
-            point_t pstart, pend;
+            point_t pstart = {0,0};
+            point_t pend = {0,0};
             if (istart < 0 && iend < 0)
             {
                 /* No intersection found */
diff --git a/applications/demo/2d/filament_swirl/filament_swirl_split.cpp b/applications/demo/2d/filament_swirl/filament_swirl_split.cpp
index 31202bf44..bda2400c5 100644
--- a/applications/demo/2d/filament_swirl/filament_swirl_split.cpp
+++ b/applications/demo/2d/filament_swirl/filament_swirl_split.cpp
@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2012-2023 Carsten Burstedde, Donna Calhoun, Scott Aiton
+Copyright (c) 2012-2024 Carsten Burstedde, Donna Calhoun, Scott Aiton
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -161,7 +161,7 @@ main (int argc, char **argv)
 
         /* MPI COMMs */
         int size, rank;
-        sc_MPI_Comm mpicomm = fclaw_app_get_mpi_size_rank (app, &size, &rank);
+        fclaw_app_get_mpi_size_rank (app, &size, &rank);
 
         /* Globs */
         fclaw_global_t *filament_glob = fclaw_global_new_comm (subcomm, size, rank);
diff --git a/applications/demo/2d/filament_swirl/user_run.c b/applications/demo/2d/filament_swirl/user_run.c
index a43343f5e..4b8525854 100644
--- a/applications/demo/2d/filament_swirl/user_run.c
+++ b/applications/demo/2d/filament_swirl/user_run.c
@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2012-2022 Carsten Burstedde, Donna Calhoun, Scott Aiton
+Copyright (c) 2012-2024 Carsten Burstedde, Donna Calhoun, Scott Aiton
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -301,210 +301,6 @@ double outstyle_1(outstyle_1_context_t* ctx, double t_pause, fclaw_global_t *glo
     return ctx->final_time;
 }
 
-static
-void outstyle_3(fclaw_global_t *glob)
-{
-    fclaw_domain_t** domain = &glob->domain;
-
-    int init_flag = 1;
-    fclaw_diagnostics_gather(glob,init_flag);
-    init_flag = 0;
-
-    int iframe = 0;
-    fclaw_output_frame(glob,iframe);
-
-
-    const fclaw_options_t *fclaw_opt = fclaw_get_options(glob);
-    double initial_dt = fclaw_opt->initial_dt;
-
-
-    //fclaw2d_time_sync_reset(glob,fclaw_opt->minlevel,fclaw_opt->maxlevel,1);
-
-    double t0 = 0;
-    double dt_minlevel = initial_dt;
-    glob->curr_time = t0;
-    int nstep_outer = fclaw_opt->nout;
-    int nstep_inner = fclaw_opt->nstep;
-    int nregrid_interval = fclaw_opt->regrid_interval;
-    int level_factor = pow_int(2,fclaw_opt->maxlevel-fclaw_opt->minlevel);
-    if (!fclaw_opt->subcycle)
-    {
-        if (fclaw_opt->advance_one_step)
-        {
-            if (!fclaw_opt->outstyle_uses_maxlevel)
-            {
-                /* Multiply nout/nstep by 2^(maxlevel-minlevel) so that
-                   a given nout/nstep pair works for both subcycled
-                   and non-subcycled cases.
-                   Note : Regrid_interval remains unchanged.*/
-
-                nstep_outer *= level_factor;
-                nstep_inner *= level_factor;  /* Only produce nout/nstep output files */
-            }
-        }
-    }
-
-    int n = 0;
-    double t_curr = t0;
-    while (n < nstep_outer)
-    {
-        double dt_step = dt_minlevel;
-        if (!fclaw_opt->subcycle && fclaw_opt->advance_one_step)
-        {
-            /* if domain->global_maxlevel < fclaw_opt->maxlevel, this choice
-               of time step will take more steps than necessary on
-               finest level.  */
-            dt_step /= level_factor;
-        }
-
-        /* In case we have to reject this step */
-        if (!fclaw_opt->use_fixed_dt)
-        {
-            save_time_step(glob);
-        }
-
-        /* Get current domain data since it may change during regrid */
-        glob->curr_dt = dt_step;
-        double maxcfl_step = fclaw_advance_all_levels(glob, t_curr,dt_step);
-
-        /* This is a collective communication - everybody needs to wait here. */
-        if (fclaw_opt->reduce_cfl)
-        {
-            /* If we are taking a variable time step, we have to reduce the 
-               maxcfl so that every processor takes the same size dt */
-            fclaw_timer_start (&glob->timers[FCLAW_TIMER_CFL_COMM]);
-            maxcfl_step = fclaw_domain_global_maximum (*domain, maxcfl_step);
-            fclaw_timer_stop (&glob->timers[FCLAW_TIMER_CFL_COMM]);     
-        }
-
-        double tc = t_curr + dt_step;
-        int level2print = (fclaw_opt->advance_one_step && fclaw_opt->outstyle_uses_maxlevel) ?
-                          fclaw_opt->maxlevel : fclaw_opt->minlevel;
-
-        fclaw_global_productionf("Level %d (%d-%d) step %5d : dt = %12.3e; maxcfl (step) = " \
-                                 "%12.6f; Final time = %12.4f\n",
-                                 level2print,
-                                 (*domain)->global_minlevel,
-                                 (*domain)->global_maxlevel,
-                                 n+1,dt_step,maxcfl_step, tc);
-
-        if (fclaw_opt->reduce_cfl & (maxcfl_step > fclaw_opt->max_cfl))
-        {
-            if (!fclaw_opt->use_fixed_dt)
-            {
-                fclaw_global_productionf("   WARNING : Maximum CFL exceeded; retaking time step\n");
-                restore_time_step(glob);
-
-                dt_minlevel = dt_minlevel*fclaw_opt->desired_cfl/maxcfl_step;
-
-                /* Go back to start of loop without incrementing step counter or
-                   current time. */
-                continue;
-            }
-            else
-            {
-                fclaw_global_productionf("   WARNING : Maximum CFL exceeded\n");
-            }
-        }
-
-        /* We are happy with this time step */
-        t_curr = tc;
-        glob->curr_time = t_curr;
-
-        /* New time step, which should give a cfl close to the desired cfl. */
-        if (!fclaw_opt->use_fixed_dt)
-        {
-            dt_minlevel = dt_minlevel*fclaw_opt->desired_cfl/maxcfl_step;
-        }
-
-        n++;  /* Increment outer counter */
-
-        if (fclaw_opt->regrid_interval > 0)
-        {
-            if (n % nregrid_interval == 0)
-            {
-                fclaw_global_infof("regridding at step %d\n",n);
-                fclaw_regrid(glob);
-            }
-        }
-
-        if (fclaw_opt->advance_one_step)
-        {
-            //fclaw2d_diagnostics_gather(glob,init_flag);
-        }
-
-        if (n % nstep_inner == 0)
-        {
-            iframe++;
-            fclaw_diagnostics_gather(glob,init_flag);
-            fclaw_output_frame(glob,iframe);
-        }
-    }
-}
-
-
-static
-void outstyle_4(fclaw_global_t *glob)
-{
-
-    /* Write out an initial time file */
-    int iframe = 0;
-    fclaw_output_frame(glob,iframe);
-
-    int init_flag = 1;
-    fclaw_diagnostics_gather(glob,init_flag);
-    init_flag = 0;
-
-    const fclaw_options_t *fclaw_opt = fclaw_get_options(glob);
-    double initial_dt = fclaw_opt->initial_dt;
-    int nstep_outer = fclaw_opt->nout;
-    int nstep_inner = fclaw_opt->nstep;
-    double dt_minlevel = initial_dt;
-
-    double t0 = 0;
-    double t_curr = t0;
-    glob->curr_time = t_curr;
-    int n = 0;
-    while (n < nstep_outer)
-    {
-        /* Get current domain data since it may change during regrid */
-        fclaw_advance_all_levels(glob, t_curr, dt_minlevel);
-
-        int level2print = (fclaw_opt->advance_one_step && fclaw_opt->outstyle_uses_maxlevel) ?
-                          fclaw_opt->maxlevel : fclaw_opt->minlevel;
-
-        fclaw_global_productionf("Level %d step %5d : dt = %12.3e; Final time = %16.6e\n",
-                                 level2print,
-                                 n+1,dt_minlevel, t_curr+dt_minlevel);
-
-        t_curr += dt_minlevel;
-        n++;
-
-        glob->curr_time = t_curr;
-
-        if (fclaw_opt->regrid_interval > 0)
-        {
-            if (n % fclaw_opt->regrid_interval == 0)
-            {
-                fclaw_global_infof("regridding at step %d\n",n);
-
-                fclaw_regrid(glob);
-            }
-        }
-        else
-        {
-            /* Only use the initial grid */
-        }
-
-        if (n % nstep_inner == 0)
-        {
-            fclaw_diagnostics_gather(glob,init_flag);
-            iframe++;
-            fclaw_output_frame(glob,iframe);
-        }
-    }
-}
-
 
 /* ------------------------------------------------------------------
    Public interface

From 402d2040ae8288f02f00b89ac00fe79ceaff9107 Mon Sep 17 00:00:00 2001
From: donnaaboise <donna.calhoun@gmail.com>
Date: Mon, 22 Jul 2024 16:02:21 -0700
Subject: [PATCH 24/24] (demo/restart) Remove swirl_ray file

---
 applications/demo/2d/swirl_restart/Makefile.am | 1 -
 1 file changed, 1 deletion(-)

diff --git a/applications/demo/2d/swirl_restart/Makefile.am b/applications/demo/2d/swirl_restart/Makefile.am
index 1aef69e75..93aab65a1 100644
--- a/applications/demo/2d/swirl_restart/Makefile.am
+++ b/applications/demo/2d/swirl_restart/Makefile.am
@@ -5,7 +5,6 @@ bin_PROGRAMS += applications/demo/2d/swirl_restart/swirl
 applications_demo_2d_swirl_restart_swirl_SOURCES = \
 	applications/demo/2d/swirl_restart/swirl_user.cpp \
 	applications/demo/2d/swirl_restart/swirl_user.h \
-	applications/demo/2d/swirl_restart/swirl_ray.c \
 	applications/demo/2d/swirl_restart/swirl_options.c \
 	applications/demo/2d/swirl_restart/swirl.cpp \
 	applications/demo/2d/swirl_restart/psi.f \